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- PDB-2bdc: Porcine pancreatic elastase complexed with Asn-Pro-Ile at pH 5.0 -

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Basic information

Entry
Database: PDB / ID: 2bdc
TitlePorcine pancreatic elastase complexed with Asn-Pro-Ile at pH 5.0
ComponentsElastase-1
KeywordsHYDROLASE / SERINE PROTEINASE
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, B. / Schofield, C.J. / Wilmouth, R.C.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Structural analyses on intermediates in serine protease catalysis
Authors: Liu, B. / Schofield, C.J. / Wilmouth, R.C.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of a specific acyl-enzyme complex formed between beta-casomorphin-7 and porcine pancreatic elastase
Authors: Wilmouth, R.C. / Clifton, I.J. / Robinson, C.V. / Roach, P.L. / Aplin, R.T. / Westwood, N.J. / Hajdu, J. / Schofield, C.J.
#2: Journal: Nat.Struct.Biol. / Year: 2001
Title: X-ray snapshots of serine protease catalysis reveal a tetrahedral intermediate
Authors: Wilmouth, R.C. / Edman, K. / Neutze, R. / Wright, P.A. / Clifton, I.J. / Schneider, T.R. / Schofield, C.J. / Hajdu, J.
#3: Journal: J.BIOL.CHEM. / Year: 2002
Title: X-ray structure of a serine protease acyl-enzyme complex at 0.95-A resolution
Authors: Katona, G. / Wilmouth, R.C. / Wright, P.A. / Berglund, G.I. / Hajdu, J. / Neutze, R. / Schofield, C.J.
History
DepositionOct 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elastase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0643
Polymers25,9281
Non-polymers1362
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.145, 57.874, 74.529
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Elastase-1


Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONFLICT IS BASED ON THE REFERENCE 3 IN SEQUENCE DATABASE, P00772 IN SWISS-PROT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 17.5 MG/ML NPI, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 127 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 26, 2005 / Details: OSMIC mirrors
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→19.58 Å / Num. obs: 19783 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 34.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 23.2 / Num. unique all: 2737 / % possible all: 93.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EST

3est


Resolution: 1.8→19.58 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.798 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The peptide ASN-PRO-ILE was not modelled into the structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1024 5.2 %RANDOM
Rwork0.177 ---
all0.179 19783 --
obs0.179 19755 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.992 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 6 124 1932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211850
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9172535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9185239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02824.23178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24415266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.919159
X-RAY DIFFRACTIONr_chiral_restr0.0980.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021416
X-RAY DIFFRACTIONr_nbd_refined0.1990.2844
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21269
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0880.2121
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.210
X-RAY DIFFRACTIONr_mcbond_it2.03321206
X-RAY DIFFRACTIONr_mcangle_it2.78531902
X-RAY DIFFRACTIONr_scbond_it4.0814756
X-RAY DIFFRACTIONr_scangle_it4.8786633
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 74 -
Rwork0.167 1311 -
all-1385 -
obs--92.7 %
Refinement TLS params.Method: refined / Origin x: -4.169 Å / Origin y: 28.237 Å / Origin z: 42.915 Å
111213212223313233
T-0.0775 Å2-0.0054 Å2-0.0037 Å2--0.0785 Å2-0.01 Å2---0.0625 Å2
L0.9512 °20.076 °2-0.0323 °2-0.6108 °2-0.0736 °2--1.1571 °2
S-0.0005 Å °0.0015 Å °-0.0305 Å °-0.0088 Å °-0.0069 Å °-0.0083 Å °0.0459 Å °0.0138 Å °0.0074 Å °
Refinement TLS groupSelection: ALL

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